Link at https://docs.google.com/document/d/1bdNeOMAYY90k8FAbPRWGBgS1YBEdP09kP0vcW0tNgPc/edit?usp=sharing
european <- read_csv("01-cleaning_data_data/european_recoded.csv")
australian <- read_csv("01-cleaning_data_data/australian_recoded.csv")
dim(european)
[1] 209 115
dim(australian)
[1] 269 146
european$EU <- 1
australian$AU <- 1
all <- merge(european,australian,all = TRUE)
table(all$EU,all$AU,useNA = "always")
1 <NA>
1 0 209
<NA> 269 0
demographics_var <- c("Age","Gender","L1","speak.other.L2","study.other.L2","origins","year.studyL2","other5.other.ways","degree","roleL2.degree","study.year","prof","L2.VCE","uni1.year","Context")
l2School <- "\\.L2school$"
l2School_variables <- colnames(all)[grep(l2School,colnames(all))]
#table(all$L1,all$Context) # too many levels - needs to be cleaned (ex tot number of languages?)
table(all$L1,useNA = "always")
Afrikaans Albanian Burmese Cantonese Chinese Croatian Dutch
1 2 1 4 7 1 1
English English and Dutch German German and English German and Turkish I Indonesian
201 2 77 2 1 1 1
Italian Japanese Mandarin Persian Persian (Farsi) Romanian Russian
89 1 5 1 1 3 2
Sindhi Slovak Spanish Turkish Ukrainian <NA>
1 1 3 1 1 67
ggplot(all,aes(x=L1,fill=Context)) + geom_bar() + coord_flip() + ggtitle("First Language") + labs(y="N. of participants",x="")+theme_bw()
#table(all$speak.other.L2,all$Context)
L2 <- data.frame(Freq=table(all$speak.other.L2)[order(table(all$speak.other.L2),decreasing = TRUE)],
L2=names(table(all$speak.other.L2))[order(table(all$speak.other.L2),decreasing = TRUE)]) # too many levels - needs to be cleaned (ex tot number of languages?)
head(L2)
table(all$origins,useNA = "always")
No Yes <NA>
323 89 66
table(all$year.studyL2)
0 years 1- 3 years 1-3 years 4-6 years
69 12 11 61
First year of primary school Kindergarten Less than a year more than 6 years
80 30 27 49
Other
72
table(all$degree)
BA in Anglistik BA in Nordamerikastudien HUM
43 4 129
HUM.SCI LA Lingue e letterature straniere
6 36 82
Lingue, mercati e culture dell'Asia QC SCI
13 5 86
all$study.year[is.na(all$study.year)] <- all$uni1.year[is.na(all$study.year)]
#table(all$study.year)
all$study.year <- ifelse(all$study.year == "Already graduated after 5 semesters in March 2016, was interested in survery/study, sorry.","6th semester",all$study.year)
table(all$study.year)
1st semester 1st year 2nd semester 2nd year 3rd semester 3rd year 3rd year of Master
72 255 5 37 5 20 1
4th year bachelor 5th semester 6th semester 7th year Master
8 2 3 1 3
table(all$prof,useNA = "always")
Advanced Elementary Intermediate Upper-intermediate <NA>
78 105 84 146 65
all$study.year[is.na(all$study.year)] <- all$uni1.year[is.na(all$study.year)]
# Filter only subject that we want to include in the study
# names(table(all$study.year))[1] = 1st semester"
filtered <- subset(all, (study.year == "1st year") | (study.year == names(table(all$study.year))[1]) & year.studyL2 != "0 years")
table(filtered$Context)
English in Germany English in Italy German in Australia Italian in Australia
71 91 89 75
table(all$Context)
English in Germany English in Italy German in Australia Italian in Australia
96 113 146 123
all <- filtered
demographics_var <- c("Age","Gender","L1","speak.other.L2","study.other.L2","origins","year.studyL2","other5.other.ways","degree","roleL2.degree","study.year","prof","L2.VCE","uni1.year","Context")
l2School <- "\\.L2school$"
l2School_variables <- colnames(all)[grep(l2School,colnames(all))]
ggplot(all,aes(x=L1,fill=Context)) + geom_bar() + coord_flip() + ggtitle("First Language") + labs(y="N. of participants",x="") + theme_bw()
table(all$L1,all$Context)
English in Germany English in Italy German in Australia Italian in Australia
Afrikaans 0 0 1 0
Albanian 0 1 0 0
Cantonese 0 0 2 0
Chinese 0 2 2 0
Dutch 1 0 0 0
English 1 0 75 73
English and Dutch 0 0 2 0
German 64 0 0 0
German and English 1 0 1 0
I 0 0 0 1
Indonesian 0 0 1 0
Italian 0 87 0 0
Japanese 0 0 1 0
Mandarin 0 0 1 1
Persian (Farsi) 0 0 1 0
Romanian 0 0 1 0
Russian 2 0 0 0
Sindhi 0 0 1 0
Spanish 1 0 0 0
Turkish 1 0 0 0
Ukrainian 0 1 0 0
table(all$degree,all$L1)
Afrikaans Albanian Cantonese Chinese Dutch English English and Dutch German German and English I
BA in Anglistik 0 0 0 0 0 1 0 34 1 0
BA in Nordamerikastudien 0 0 0 0 0 0 0 4 0 0
HUM 1 0 2 0 0 92 1 0 0 1
HUM.SCI 0 0 0 0 0 5 0 0 0 0
LA 0 0 0 0 1 0 0 25 0 0
Lingue e letterature straniere 0 1 0 1 0 0 0 0 0 0
Lingue, mercati e culture dell'Asia 0 0 0 1 0 0 0 0 0 0
QC 0 0 0 0 0 4 0 0 0 0
SCI 0 0 0 2 0 45 1 0 1 0
Indonesian Italian Japanese Mandarin Persian (Farsi) Romanian Russian Sindhi Spanish Turkish Ukrainian
BA in Anglistik 0 0 0 0 0 0 2 0 1 0 0
BA in Nordamerikastudien 0 0 0 0 0 0 0 0 0 0 0
HUM 0 0 0 0 0 0 0 0 0 0 0
HUM.SCI 0 0 0 0 0 0 0 0 0 0 0
LA 0 0 0 0 0 0 0 0 0 1 0
Lingue e letterature straniere 0 75 0 0 0 0 0 0 0 0 1
Lingue, mercati e culture dell'Asia 0 12 0 0 0 0 0 0 0 0 0
QC 0 0 0 0 0 0 0 0 0 0 0
SCI 1 0 1 2 1 1 0 1 0 0 0
#Filter by L1
nc <- names(table(all$Context))
table(all$Context)
English in Germany English in Italy German in Australia Italian in Australia
71 91 89 75
l1_filter <- all[(all$Context == nc[1] & (all$L1 == "German" | all$L1 == "German and English")) |
(all$Context == nc[2] & (all$L1 == "Italian")) |
(all$Context == nc[3] & (all$L1 == "English" | all$L1 == "English and Dutch" | all$L1 == "German and English")) |
(all$Context == nc[4] & (all$L1 == "English" | all$L1 == "English and Dutch" | all$L1 == "German and English")),]
#all <- l1_filter
# do not filter for L1
all <- all
# subset demographics
demo <- subset(all,select=c("Resp.ID",demographics_var,l2School_variables))
# Numeri finali
table(l1_filter$Context)
English in Germany English in Italy German in Australia Italian in Australia
65 87 78 73
table(all$Context)
English in Germany English in Italy German in Australia Italian in Australia
71 91 89 75
missing_bySample <- rowSums(is.na(demo))
names(missing_bySample) <- demo$Resp.ID
missing_byVar <- colSums(is.na(demo))
names(missing_byVar) <- colnames(demo)
barplot(missing_bySample)
d <- data.frame(miss=missing_byVar)
d$varID <- rownames(d)
ggplot(data=d,aes(x=varID,y=miss)) + geom_bar(stat="identity") + theme_bw() +theme(axis.text.x = element_text(angle = 45, hjust = 1))
demo_missing <- demo %>% group_by(Context) %>% summarise(roleL2.degree_na = sum(is.na(roleL2.degree)),
L2.VCE_na = sum(is.na(L2.VCE)),
other5.other.ways_na=sum(is.na(other5.other.ways )),
uni1.year_na = sum(is.na(uni1.year)),
primary1.L2school_na=sum(is.na(primary1.L2school)),
CLS3.L2school_na = sum(is.na(CLS3.L2school)),
VSL4.L2school_na=sum(is.na(VSL4.L2school)),
degree = sum(is.na(degree)),
schooL2country5.L2school_na=sum(is.na(schooL2country5.L2school)))
# We do not filter for speak.other.L2 or study.other.L2
#demo[is.na(demo$speak.other.L2),]
# teniamo
#demo[is.na(demo$study.other.L2),]
missing_bySample[names(missing_bySample) == "5166861581"]
5166861581
10
#demo[is.na(demo$year.studyL2),]
missing_bySample[names(missing_bySample) == "5378798787"]
5378798787
3
# remove NA from degree
#table(demo$degree,useNA = "always")
# Remove people
all <- all[!is.na(all$degree),]
table(all$Context)
English in Germany English in Italy German in Australia Italian in Australia
70 91 88 74
write.csv(all,file.path("02-descriptive_data/context-merged_filtered.csv"))
# add numbers on the bar
# tabAge <- t(table(all$Age,all$Context))
# ggplot(all,aes(x=Age,fill=Context)) + geom_bar(position="dodge",colour="white") + labs(y="N participants") + scale_y_continuous(breaks=seq(0,90,10),limits=c(0,90)) + theme_bw() + draw_grob(tableGrob(tabAge), x=2.5, y=40, width=0.3, height=0.4) + ggtitle("Participants by age")
# tabAge
tabAge <- t(table(all$Age,all$Context))
ggdf <- data.frame(Age = rep(colnames(tabAge),each=4)[!(as.numeric(tabAge) == 0)],
N.Participants = as.numeric(tabAge)[!(as.numeric(tabAge) == 0)],
Context = rep(rownames(tabAge),times=3)[!(as.numeric(tabAge) == 0)])
ggplot(ggdf,aes(x=Age,y=N.Participants,fill=Context)) + geom_bar(position="dodge",colour="white",stat="identity") + scale_y_continuous(breaks=seq(0,90,10),limits=c(0,90)) + theme_bw() + ggtitle("Participants by age")+
geom_text(aes(label = N.Participants), hjust=0.5, vjust=-0.25, size = 2.5,position=position_dodge(width=0.9))
# add numbers on the bar
tabAge <- t(table(all$Gender,all$Context))
ggdf <- data.frame(Gender = rep(colnames(tabAge),each=4)[!(as.numeric(tabAge) == 0)],
N.Participants = as.numeric(tabAge)[!(as.numeric(tabAge) == 0)],
Context = rep(rownames(tabAge),times=3)[!(as.numeric(tabAge) == 0)])
ggplot(ggdf,aes(x=Gender,y=N.Participants,fill=Context)) + geom_bar(position="dodge",colour="white",stat="identity") + labs(y="N participants") + scale_y_continuous(breaks=seq(0,90,10),limits=c(0,90)) + theme_bw() + ggtitle("Participants by gender")+ geom_text(aes(label = N.Participants), hjust=0.5, vjust=-0.25, size = 2.5,position=position_dodge(width=0.9))
# add numbers on the bar
tabAge <- t(table(all$origins,all$Context))
ggplot(all,aes(x=origins,fill=Context)) + geom_bar(position="dodge",colour="white") + ggtitle("Origins by context") + scale_y_continuous(breaks=seq(0,90,10),limits=c(0,90)) + theme_bw() + draw_grob(tableGrob(tabAge), x=2, y=60, width=0.3, height=0.4) + ggtitle("Participants by origins")
tabAge
No Yes
English in Germany 65 5
English in Italy 90 1
German in Australia 63 25
Italian in Australia 36 38
tabAge <- t(table(all$prof,all$Context))
ggplot(all,aes(x=Context,fill=prof)) + geom_bar(position="dodge",colour="white") + ggtitle("Proficiency by context") + scale_y_continuous(breaks=seq(0,90,10),limits=c(0,90)) + theme_bw() + draw_grob(tableGrob(tabAge), x=2, y=80, width=0.3, height=0.4)
tabAge
Advanced Elementary Intermediate Upper-intermediate
English in Germany 38 0 5 27
English in Italy 23 2 9 57
German in Australia 4 32 25 27
Italian in Australia 0 29 29 16
tabAge <- t(table(all[all$Context != "English in Germany" & all$Context != "English in Italy","L2.VCE"],all[all$Context != "English in Germany" & all$Context != "English in Italy",'Context'],useNA = "always"))
tabAge <- tabAge[-3,]
ggplot(all[all$Context != "English in Germany" & all$Context != "English in Italy",],aes(x=Context,fill=L2.VCE)) + geom_bar(position="dodge",colour="white") + ggtitle("L2.VCE by context") + scale_y_continuous(breaks=seq(0,90,10),limits=c(0,90)) + theme_bw() + draw_grob(tableGrob(tabAge), x=2, y=80, width=0.3, height=0.4)
# year study L2
table(all$year.studyL2,all$other.year.studyL2.richi)
BILINGUAL FIRST.YEAR.SECONDARY FOURTH.YEAR.PRIMARY LOWER.SECONDARY PERSONAL SECOND.YEAR.PRIMARY
0 years 0 0 0 0 0 0
1- 3 years 0 0 0 0 0 0
1-3 years 0 0 0 0 0 0
4-6 years 0 0 0 0 0 0
First year of primary school 0 0 0 0 0 0
Kindergarten 0 0 0 0 0 0
Less than a year 0 0 0 0 0 0
more than 6 years 0 0 0 0 0 0
Other 4 10 5 4 2 2
SECOND.YEAR.SECONDARY THIRD.YEAR.PRIMARY
0 years 0 0
1- 3 years 0 0
1-3 years 0 0
4-6 years 0 0
First year of primary school 0 0
Kindergarten 0 0
Less than a year 0 0
more than 6 years 0 0
Other 2 28
all$year.studyL2 <- ifelse(all$year.studyL2 == "Other",all$other.year.studyL2.richi,all$year.studyL2 )
# European context
ggplot(all[all$Context == "English in Germany" | all$Context == "English in Italy",],aes(x=degree,fill=year.studyL2)) + geom_bar(position="dodge",colour="white") + theme_bw() + ggtitle("Degree by study year L2, by Context") + facet_grid(~Context,scales="free") + theme(axis.text.x = element_text(angle = 45, hjust = 1)) + labs(y = "N participants", x = "degree")
# Australian context
tabAge <- t(table(all[all$Context == "Italian in Australia" | all$Context == "German in Australia",'degree'],all[all$Context == "Italian in Australia" | all$Context == "German in Australia",'Context']))
ggplot(all[all$Context == "Italian in Australia" | all$Context == "German in Australia",],aes(x=Context,fill=degree)) + geom_bar(position="dodge",colour="white") + theme_bw() + ggtitle("Degree in Australian Contexts") + draw_grob(tableGrob(tabAge), x=1., y=40, width=0.3, height=0.4)
tabAge
HUM HUM.SCI QC SCI
German in Australia 47 3 4 34
Italian in Australia 50 2 0 22
# Australian context
tabAge <- t(table(all[all$Context == "English in Italy" | all$Context == "English in Germany",'degree'],all[all$Context == "English in Italy" | all$Context == "English in Germany",'Context']))
ggplot(all[all$Context == "English in Italy" | all$Context == "English in Germany",],aes(x=Context,fill=degree)) + geom_bar(position="dodge",colour="white") + theme_bw() + ggtitle("Degree in European Contexts")
tabAge
BA in Anglistik BA in Nordamerikastudien LA Lingue e letterature straniere Lingue, mercati e culture dell'Asia
English in Germany 39 4 27 0 0
English in Italy 0 0 0 78 13
all_melt <- melt(all,id.vars = c("Resp.ID","Gender","Age","prof","Context","study.year"),
measure.vars = likert_variables_all)
all_melt$value <- factor(all_melt$value,levels=c("Strongly disagree","Disagree","Not sure","Agree","Strongly agree"))
all_melt <- all_melt %>% separate(variable,into=c("item","type"),sep="\\.",remove=FALSE)
Too few values at 646 locations: 9368, 9369, 9370, 9371, 9372, 9373, 9374, 9375, 9376, 9377, 9378, 9379, 9380, 9381, 9382, 9383, 9384, 9385, 9386, 9387, ...
ggplot(all_melt,aes(x=variable,fill=value)) + geom_bar(position = "stack",colour="black") +
facet_grid(Context~type,scales = "free")+theme(axis.text.x = element_text(angle = 45, hjust = 1),axis.text=element_text(size=8)) + ggtitle("Filtered dataset") + scale_fill_manual(values=c("#ca0020","#f4a582","#ffffbf","#abd9e9","#2c7bb6","grey"))
filt_sum <- all_melt %>% group_by(Context,variable,type,value) %>% dplyr::summarise(Ngroup=length(value))
ggplot(filt_sum,aes(x=value,y=Ngroup,colour=Context,group=interaction(variable, Context))) + geom_line() + geom_point() + facet_wrap(~type,scales = "free")+theme(axis.text.x = element_text(angle = 45, hjust = 1))
convertToNumber <- function(column){
column <- factor(column,levels = c("Strongly disagree","Disagree","Not sure","Agree","Strongly agree"))
column_number <- as.numeric(column)
return(column_number)
}
table(all$Context)
English in Germany English in Italy German in Australia Italian in Australia
70 91 88 74
convert_likert <- data.frame(apply(subset(all,select=likert_variables_all),2,convertToNumber))
colnames(convert_likert) <- paste0(colnames(convert_likert),"1")
likert_variables1 <- paste0(likert_variables_all,"1")
# join the converted variables to the filtered dataset
filtered_conv <- cbind(all,convert_likert)
table(filtered_conv[,likert_variables_all[4]],filtered_conv[,likert_variables1[4]],useNA = "always")
1 2 3 4 5 <NA>
Agree 0 0 0 121 0 0
Disagree 0 10 0 0 0 0
Not sure 0 0 39 0 0 0
Strongly agree 0 0 0 0 152 0
Strongly disagree 1 0 0 0 0 0
<NA> 0 0 0 0 0 0
write.csv(filtered_conv,"02-descriptive_data/merged_filtered_likertNumber.csv",row.names = FALSE)
cov <- cor(filtered_conv[filtered_conv$Context == "Italian in Australia",likert_variables1[!(likert_variables1 %in% "necessity1")]],method = "pearson",use="pairwise.complete.obs")
row_infos <- data.frame(Variables=sapply(strsplit(colnames(cov),split="\\."),function(x) x[2]))
row_infos$Variables <- as.character(row_infos$Variables)
rownames(row_infos) <- rownames(cov)
row_infos$Variables[which(is.na(row_infos$Variables))] <- c("educated")
row_infos <- row_infos[order(row_infos$Variables),,drop=FALSE]
ann_col_wide <- data.frame(Variable=unique(row_infos$Variables))
ann_colors_wide <- list(Variables=c(comm1="#bd0026",educated="#b35806", id1="#f6e8c3",instru1="#35978f",integr1="#386cb0",intr1="#ffff99",ought1="grey",post1="black",prof1="pink"))
#pheatmap(cov, main = "Italian in Australia",annotation_names_row = FALSE,cluster_cols=TRUE,cluster_rows=TRUE,annotation_col = row_infos[,1,drop=FALSE], annotation_row = row_infos[,1,drop=FALSE], annotation_colors = ann_colors_wide,breaks=seq(-1,1,0.2),col=c("#67001f","#b2182b","#d6604d","#f4a582","#fddbc7","#f7f7f7","#d1e5f0","#92c5de","#4393c3","#2166ac","#053061"),show_colnames = FALSE,width = 7,height = 7)
###################
diag(cov) <- NA
pheatmap(cov, main = "Italian in Australia",annotation_names_row = FALSE,cluster_cols=TRUE,cluster_rows=TRUE,annotation_col = row_infos[,1,drop=FALSE], annotation_row = row_infos[,1,drop=FALSE]
, annotation_colors = ann_colors_wide,show_colnames = FALSE,breaks = seq(-0.6,0.7,length.out = 50),width = 7,height = 7,color=colorRampPalette(brewer.pal(n = 7, name = "RdBu"))(50))
cov <- cor(filtered_conv[filtered_conv$Context == "German in Australia",likert_variables1[!(likert_variables1 %in% "necessity1")]],method = "pearson",use="pairwise.complete.obs")
row_infos <- data.frame(Variables=sapply(strsplit(colnames(cov),split="\\."),function(x) x[2]))
row_infos$Variables <- as.character(row_infos$Variables)
rownames(row_infos) <- rownames(cov)
row_infos$Variables[which(is.na(row_infos$Variables))] <- c("educated")
row_infos <- row_infos[order(row_infos$Variables),,drop=FALSE]
ann_col_wide <- data.frame(Variable=unique(row_infos$Variables))
ann_colors_wide <- list(Variables=c(comm1="#bd0026",educated="#b35806", id1="#f6e8c3",instru1="#35978f",integr1="#386cb0",intr1="#ffff99",ought1="grey",post1="black",prof1="pink"))
diag(cov) <- NA
pheatmap(cov, main = "German in Australia",annotation_names_row = FALSE,cluster_cols=TRUE,cluster_rows=TRUE,annotation_col = row_infos[,1,drop=FALSE], annotation_row = row_infos[,1,drop=FALSE]
, annotation_colors = ann_colors_wide,show_colnames = FALSE,breaks = seq(-0.6,0.7,length.out = 50),width = 7,height = 7,color=colorRampPalette(brewer.pal(n = 7, name = "RdBu"))(50))
cov <- cor(filtered_conv[filtered_conv$Context == "English in Germany",likert_variables1[!(likert_variables1 %in% c("reconnect.comm1", "speakersmelb.comm1","comecloser.comm1","educated1"))]],method = "pearson",use="pairwise.complete.obs")
row_infos <- data.frame(Variables=sapply(strsplit(colnames(cov),split="\\."),function(x) x[2]))
row_infos$Variables <- as.character(row_infos$Variables)
rownames(row_infos) <- rownames(cov)
row_infos$Variables[which(is.na(row_infos$Variables))] <- c("necessity")
row_infos <- row_infos[order(row_infos$Variables),,drop=FALSE]
ann_col_wide <- data.frame(Variable=unique(row_infos$Variables))
ann_colors_wide <- list(Variables=c(id1="#f6e8c3",necessity="#b35806",instru1="#35978f",integr1="#386cb0",intr1="#ffff99",ought1="grey",post1="black",prof1="pink"))
diag(cov) <- NA
pheatmap(cov, main = "English in Germany",annotation_names_row = FALSE,cluster_cols=TRUE,cluster_rows=TRUE,annotation_col = row_infos[,1,drop=FALSE], annotation_row = row_infos[,1,drop=FALSE]
, annotation_colors = ann_colors_wide,show_colnames = FALSE,breaks = seq(-0.6,0.7,length.out = 50),width = 7,height = 7,color=colorRampPalette(brewer.pal(n = 7, name = "RdBu"))(50))
cov <- cor(filtered_conv[filtered_conv$Context == "English in Italy",likert_variables1[!(likert_variables1 %in% c("reconnect.comm1","speakersmelb.comm1","comecloser.comm1","educated1"))]],method = "pearson",use="pairwise.complete.obs")
row_infos <- data.frame(Variables=sapply(strsplit(colnames(cov),split="\\."),function(x) x[2]))
row_infos$Variables <- as.character(row_infos$Variables)
rownames(row_infos) <- rownames(cov)
row_infos$Variables[which(is.na(row_infos$Variables))] <- "necessity"
row_infos <- row_infos[order(row_infos$Variables),,drop=FALSE]
ann_col_wide <- data.frame(Variable=unique(row_infos$Variables))
ann_colors_wide <- list(Variables=c(comm1="#bd0026",necessity="#b35806", id1="#f6e8c3",instru1="#35978f",integr1="#386cb0",intr1="#ffff99",ought1="grey",post1="black",prof1="pink"))
diag(cov) <- NA
pheatmap(cov, main = "English in Italy",annotation_names_row = FALSE,cluster_cols=TRUE,cluster_rows=TRUE,annotation_col = row_infos[,1,drop=FALSE], annotation_row = row_infos[,1,drop=FALSE]
, annotation_colors = ann_colors_wide,show_colnames = FALSE,breaks = seq(-0.6,0.7,length.out = 50),width = 7,height = 7,color=colorRampPalette(brewer.pal(n = 7, name = "RdBu"))(50))
cov <- cor(filtered_conv[,likert_variables1],method = "pearson",use="pairwise.complete.obs")
row_infos <- data.frame(Variables=sapply(strsplit(colnames(cov),split="\\."),function(x) x[2]))
row_infos$Variables <- as.character(row_infos$Variables)
rownames(row_infos) <- rownames(cov)
row_infos$Variables[which(is.na(row_infos$Variables))] <- c("necessity","educated")
row_infos <- row_infos[order(row_infos$Variables),,drop=FALSE]
ann_col_wide <- data.frame(Variable=unique(row_infos$Variables))
ann_colors_wide <- list(Variables=c(comm1="#bd0026",educated="orange", id1="#f6e8c3",instru1="#35978f",necessity="#b35806",integr1="#386cb0",intr1="#ffff99",ought1="grey",post1="black",prof1="pink"))
diag(cov) <- NA
pheatmap(cov, main = "All Contexts",annotation_names_row = FALSE,cluster_cols=TRUE,cluster_rows=TRUE,annotation_col = row_infos[,1,drop=FALSE], annotation_row = row_infos[,1,drop=FALSE]
, annotation_colors = ann_colors_wide,show_colnames = FALSE,breaks = seq(-0.6,0.7,length.out = 50),width = 7,height = 7,color=colorRampPalette(brewer.pal(n = 7, name = "RdBu"))(50))
sets <- list(id.var=likert_variables1[grep("\\.id1$",likert_variables1)],
ought.var=likert_variables1[grep("\\.ought1$",likert_variables1)],
intr.var=likert_variables1[grep("\\.intr1$",likert_variables1)],
instru.var=likert_variables1[grep("\\.instru1$",likert_variables1)],
integr1.var=likert_variables1[grep("\\.integr1$",likert_variables1)],
prof.var=likert_variables1[grep("\\.prof1$",likert_variables1)],
post.var=likert_variables1[grep("\\.post1$",likert_variables1)],
comm.var=likert_variables1[grep("\\.comm1$",likert_variables1)])
get_alpha <- function(dataMot,
var=sets$id.var){
var_alpha <- alpha(dataMot[,var])
dataf <- data.frame(alpha=var_alpha$total,
drop = var_alpha$alpha.drop)
rownames(dataf) <- rownames(var_alpha$alpha.drop)
return(dataf)
}
# "Italian in Australia"
ita_in_au <- do.call(rbind,lapply(sets,function(x) {
get_alpha(data=filtered_conv[filtered_conv$Context == "Italian in Australia",],
var=x)}))
ita_in_au$var <- sapply(strsplit(rownames(ita_in_au),split="\\."),function(x) x[1])
ita_in_au$var.full <- sapply(strsplit(rownames(ita_in_au),split="\\."),function(x) x[3])
ita_in_au$Context <- "Italian in Australia"
rownames(ita_in_au) <- NULL
# "German in Australia"
germ_in_au <- do.call(rbind,lapply(sets,function(x) {
get_alpha(data=filtered_conv[filtered_conv$Context == "German in Australia",],
var=x)}))
Some items were negatively correlated with the total scale and probably
should be reversed.
To do this, run the function again with the 'check.keys=TRUE' option
Some items ( knowledge.instru1 ) were negatively correlated with the total scale and
probably should be reversed.
To do this, run the function again with the 'check.keys=TRUE' option
germ_in_au$var <- sapply(strsplit(rownames(germ_in_au),split="\\."),function(x) x[1])
germ_in_au$var.full <- sapply(strsplit(rownames(germ_in_au),split="\\."),function(x) x[3])
germ_in_au$Context <- "German in Australia"
rownames(germ_in_au) <- NULL
# "English in Germany"
eng_in_germ <- do.call(rbind,lapply(sets[!(names(sets) %in% "comm.var")],function(x) {
get_alpha(data=filtered_conv[filtered_conv$Context == "English in Germany",],
var=x)}))
Some items were negatively correlated with the total scale and probably
should be reversed.
To do this, run the function again with the 'check.keys=TRUE' option
Some items ( people.ought1 ) were negatively correlated with the total scale and
probably should be reversed.
To do this, run the function again with the 'check.keys=TRUE' option
# the ones that makes issues
get_alpha(data=filtered_conv[filtered_conv$Context == "English in Germany",],
var=sets$ought.var)
Some items were negatively correlated with the total scale and probably
should be reversed.
To do this, run the function again with the 'check.keys=TRUE' option
Some items ( people.ought1 ) were negatively correlated with the total scale and
probably should be reversed.
To do this, run the function again with the 'check.keys=TRUE' option
eng_in_germ$var <- sapply(strsplit(rownames(eng_in_germ),split="\\."),function(x) x[1])
eng_in_germ$var.full <- sapply(strsplit(rownames(eng_in_germ),split="\\."),function(x) x[3])
eng_in_germ$Context <- "English in Germany"
rownames(eng_in_germ) <- NULL
# "English in Italy"
eng_in_ita <- do.call(rbind,lapply(sets[!(names(sets) %in% "comm.var")],function(x) {
get_alpha(data=filtered_conv[filtered_conv$Context == "English in Italy",],
var=x)}))
eng_in_ita$var <- sapply(strsplit(rownames(eng_in_ita),split="\\."),function(x) x[1])
eng_in_ita$var.full <- sapply(strsplit(rownames(eng_in_ita),split="\\."),function(x) x[3])
eng_in_ita$Context <- "English in Italy"
rownames(eng_in_ita) <- NULL
# combine
full_alpha <- rbind(eng_in_ita,eng_in_germ,germ_in_au,ita_in_au)
full_alpha %>% group_by(Context,var) %>%
summarise(st.alpha = unique(alpha.std.alpha),
G6=unique(alpha.G6.smc.)) %>%
ggplot(.,aes(x=var,y=st.alpha,colour=Context)) + geom_point() + geom_line(aes(group=Context)) + theme_bw()
all_melt <- all_melt %>% separate(variable,into=c("item","type"),sep="\\.",remove=FALSE)
Too few values at 646 locations: 9368, 9369, 9370, 9371, 9372, 9373, 9374, 9375, 9376, 9377, 9378, 9379, 9380, 9381, 9382, 9383, 9384, 9385, 9386, 9387, ...
p1=ggplot(all_melt,aes(x=variable,fill=value)) + geom_bar(position = "stack") +
facet_grid(Context~type,scales = "free") + ggtitle("Filtered dataset")+theme(axis.text.x = element_text(angle = 45, hjust = 1),axis.text=element_text(size=8))+theme_bw()
p2=ggplot(full_alpha,aes(x=var.full,y=drop.std.alpha,colour=Context)) + geom_point() + geom_line(aes(group=Context)) + theme_bw() + facet_wrap(~var,scales="free")
p4=ggplot(full_alpha,aes(x=var.full,y=drop.average_r,colour=Context)) + geom_point() + geom_line(aes(group=Context)) + theme_bw() + facet_wrap(~var,scales="free")
p3=full_alpha %>% group_by(Context,var) %>%
summarise(st.alpha = unique(alpha.std.alpha),
G6=unique(alpha.G6.smc.)) %>%
ggplot(.,aes(x=var,y=st.alpha,colour=Context)) + geom_point() + geom_line(aes(group=Context)) + theme(axis.text.x = element_text(angle = 45, hjust = 1),axis.text=element_text(size=8)) + theme_bw()
cowplot::plot_grid(p2,p3,nrow=2)
all <- read.csv(file.path("02-descriptive_data/merged_filtered_likertNumber.csv"))
dat <- all[,likert_variables1[!(likert_variables1 %in% c("necessity1","educated1"))]]
psych::alpha(dat,use="pairwise.complete.obs")
Reliability analysis
Call: psych::alpha(x = dat, use = "pairwise.complete.obs")
raw_alpha std.alpha G6(smc) average_r S/N ase mean sd
0.84 0.86 0.91 0.16 6.3 0.012 3.9 0.34
lower alpha upper 95% confidence boundaries
0.82 0.84 0.87
Reliability if an item is dropped:
raw_alpha std.alpha G6(smc) average_r S/N alpha se
converse.id1 0.84 0.85 0.90 0.16 5.8 0.013
dream.id1 0.84 0.86 0.91 0.16 6.0 0.013
usewell.id1 0.84 0.86 0.91 0.16 6.1 0.013
whenever.id1 0.84 0.86 0.91 0.16 5.9 0.013
consider.ought1 0.85 0.86 0.91 0.17 6.3 0.012
people.ought1 0.84 0.86 0.91 0.17 6.2 0.013
expect.ought1 0.84 0.86 0.91 0.17 6.3 0.012
fail.ought1 0.85 0.86 0.91 0.17 6.3 0.012
enjoy.intr1 0.84 0.86 0.91 0.16 6.0 0.013
life.intr1 0.83 0.85 0.91 0.16 5.8 0.013
exciting.intr1 0.84 0.86 0.91 0.16 6.0 0.013
challenge.intr1 0.84 0.86 0.91 0.16 6.1 0.013
job.instru1 0.84 0.86 0.91 0.16 6.0 0.013
knowledge.instru1 0.84 0.86 0.91 0.17 6.1 0.013
career.instru1 0.84 0.86 0.91 0.16 6.0 0.013
money.instru1 0.84 0.86 0.91 0.17 6.1 0.013
time.integr1 0.84 0.86 0.91 0.16 6.0 0.013
becomelike.integr1 0.84 0.86 0.91 0.16 6.1 0.013
meeting.integr1 0.84 0.86 0.91 0.16 6.0 0.013
affinity.integr1 0.84 0.86 0.91 0.16 6.1 0.013
improve.prof1 0.84 0.86 0.91 0.16 6.1 0.013
speaking.prof1 0.84 0.86 0.91 0.16 6.0 0.013
reading.prof1 0.84 0.86 0.91 0.17 6.2 0.013
written.prof1 0.84 0.86 0.91 0.16 6.0 0.013
listening.prof1 0.84 0.86 0.91 0.16 6.0 0.013
citizen.post1 0.84 0.86 0.91 0.16 6.0 0.013
interact.post1 0.84 0.86 0.91 0.16 6.0 0.013
overseas.post1 0.84 0.86 0.91 0.16 5.9 0.013
globalaccess.post1 0.84 0.86 0.91 0.16 5.9 0.013
reconnect.comm1 0.85 0.86 0.91 0.17 6.2 0.012
speakersmelb.comm1 0.84 0.86 0.91 0.16 6.0 0.013
comecloser.comm1 0.84 0.86 0.91 0.17 6.1 0.013
Item statistics
n raw.r std.r r.cor r.drop mean sd
converse.id1 323 0.59 0.61 0.60 0.56 4.3 0.76
dream.id1 323 0.49 0.51 0.48 0.43 4.5 0.65
usewell.id1 323 0.42 0.42 0.39 0.34 4.3 0.72
whenever.id1 323 0.56 0.54 0.53 0.46 4.3 0.82
consider.ought1 323 0.27 0.24 0.22 0.24 2.6 1.12
people.ought1 323 0.38 0.32 0.29 0.31 3.1 1.16
expect.ought1 322 0.29 0.25 0.23 0.26 1.9 0.92
fail.ought1 323 0.29 0.24 0.21 0.22 2.1 0.96
enjoy.intr1 323 0.42 0.45 0.44 0.36 4.5 0.64
life.intr1 322 0.63 0.60 0.59 0.54 3.3 1.04
exciting.intr1 323 0.46 0.50 0.48 0.40 4.6 0.56
challenge.intr1 323 0.38 0.41 0.37 0.31 4.2 0.79
job.instru1 322 0.49 0.47 0.45 0.39 3.8 0.83
knowledge.instru1 322 0.35 0.37 0.33 0.29 4.2 0.65
career.instru1 322 0.51 0.49 0.48 0.41 4.2 0.77
money.instru1 322 0.38 0.38 0.34 0.30 3.2 0.77
time.integr1 321 0.45 0.48 0.46 0.40 4.5 0.66
becomelike.integr1 323 0.44 0.43 0.41 0.40 3.1 0.95
meeting.integr1 322 0.44 0.47 0.45 0.40 4.6 0.57
affinity.integr1 323 0.43 0.43 0.41 0.41 3.6 0.87
improve.prof1 323 0.36 0.42 0.41 0.31 4.5 0.75
speaking.prof1 323 0.40 0.46 0.46 0.35 4.7 0.53
reading.prof1 323 0.31 0.36 0.35 0.25 4.5 0.62
written.prof1 323 0.43 0.48 0.47 0.37 4.6 0.58
listening.prof1 323 0.39 0.45 0.45 0.33 4.5 0.63
citizen.post1 322 0.48 0.45 0.42 0.37 3.8 0.89
interact.post1 322 0.46 0.46 0.44 0.37 4.4 0.62
overseas.post1 323 0.50 0.53 0.51 0.43 4.6 0.58
globalaccess.post1 322 0.51 0.53 0.51 0.42 4.3 0.67
reconnect.comm1 162 0.42 0.32 0.30 0.30 2.7 1.58
speakersmelb.comm1 162 0.50 0.49 0.47 0.46 3.8 0.81
comecloser.comm1 162 0.44 0.38 0.36 0.38 3.5 0.94
Non missing response frequency for each item
1 2 3 4 5 miss
converse.id1 0.00 0.03 0.10 0.41 0.47 0.00
dream.id1 0.00 0.00 0.07 0.36 0.56 0.00
usewell.id1 0.00 0.02 0.11 0.46 0.42 0.00
whenever.id1 0.00 0.03 0.12 0.37 0.47 0.00
consider.ought1 0.14 0.40 0.21 0.19 0.06 0.00
people.ought1 0.09 0.27 0.25 0.28 0.11 0.00
expect.ought1 0.39 0.44 0.09 0.07 0.01 0.00
fail.ought1 0.27 0.46 0.16 0.10 0.01 0.00
enjoy.intr1 0.00 0.01 0.06 0.40 0.54 0.00
life.intr1 0.02 0.25 0.25 0.36 0.12 0.00
exciting.intr1 0.00 0.01 0.02 0.37 0.61 0.00
challenge.intr1 0.00 0.03 0.12 0.48 0.36 0.00
job.instru1 0.00 0.04 0.32 0.41 0.23 0.00
knowledge.instru1 0.00 0.01 0.09 0.58 0.32 0.00
career.instru1 0.00 0.00 0.20 0.40 0.39 0.00
money.instru1 0.01 0.12 0.55 0.26 0.06 0.00
time.integr1 0.00 0.01 0.07 0.30 0.63 0.01
becomelike.integr1 0.03 0.23 0.47 0.18 0.10 0.00
meeting.integr1 0.00 0.00 0.03 0.38 0.59 0.00
affinity.integr1 0.01 0.07 0.36 0.39 0.17 0.00
improve.prof1 0.01 0.02 0.03 0.34 0.59 0.00
speaking.prof1 0.00 0.01 0.00 0.28 0.71 0.00
reading.prof1 0.00 0.02 0.02 0.38 0.59 0.00
written.prof1 0.00 0.01 0.02 0.36 0.62 0.00
listening.prof1 0.00 0.01 0.04 0.38 0.57 0.00
citizen.post1 0.01 0.07 0.23 0.46 0.23 0.00
interact.post1 0.00 0.00 0.06 0.43 0.50 0.00
overseas.post1 0.00 0.01 0.02 0.34 0.63 0.00
globalaccess.post1 0.00 0.01 0.06 0.49 0.43 0.00
reconnect.comm1 0.29 0.30 0.04 0.12 0.25 0.50
speakersmelb.comm1 0.01 0.05 0.23 0.52 0.19 0.50
comecloser.comm1 0.01 0.14 0.37 0.34 0.14 0.50
#detach("package:ggplot2", unload=TRUE)
fa_all <- function(data4,rot,minL,maxL,nfac=0,seed=5){
set.seed(seed)
# Save the orignal dataset
data_orig <- data4
# Define the rotations
orth <- c("varimax", "quartimax", "bentlerT", "equamax", "varimin", "geominT" , "bifactor" )
obl <- c("Promax", "promax", "oblimin", "simplimax", "bentlerQ", "geominQ", "biquartimin" ,"cluster")
alpha2 <- function(x){
alpha.1 <- function(C, R) {
n <- dim(C)[2]
alpha.raw <- (1 - tr(C)/sum(C)) * (n/(n - 1))
sumR <- sum(R)
alpha.std <- (1 - n/sumR) * (n/(n - 1))
smc.R <- smc(R)
G6 <- (1 - (n - sum(smc.R))/sumR)
av.r <- (sumR - n)/(n * (n - 1))
mod1 <- matrix(av.r, n, n)
Res1 <- R - mod1
GF1 = 1 - sum(Res1^2)/sum(R^2)
Rd <- R - diag(R)
diag(Res1) <- 0
GF1.off <- 1 - sum(Res1^2)/sum(Rd^2)
sn <- n * av.r/(1 - av.r)
Q = (2 * n^2/((n - 1)^2 * (sum(C)^3))) * (sum(C) * (tr(C %*%
C) + (tr(C))^2) - 2 * (tr(C) * sum(C %*% C)))
result <- list(raw = alpha.raw, std = alpha.std, G6 = G6,
av.r = av.r, sn = sn, Q = Q, GF1, GF1.off)
return(result)
}
if (!isCorrelation(x)) {
item.var <- apply(x, 2, sd, na.rm = T)
bad <- which((item.var <= 0) | is.na(item.var))
if ((length(bad) > 0) && delete) {
for (baddy in 1:length(bad)) {
warning("Item = ", colnames(x)[bad][baddy], " had no variance and was deleted")
}
x <- x[, -bad]
nvar <- nvar - length(bad)
}
response.freq <- response.frequencies(x, max = 10)
C <- cov(x, use = "pairwise")
}
else {
C <- x
}
R <- cov2cor(C)
alpha.total <- alpha.1(C, R)
return(alpha.total)
}
cicl<-0
par1<-1
par2<-1
par3<-1
while(par3>0){
# Selezione il numero di fattori consigliati
cat("Calculating the number of factors needed \n")
fact <- nfac
if(nfac==0){
fact<-fa.parallel(data4)$nfact
}
if(fact==1){
stop("Only one factor remains. Check the data or reduce the threshold")
}
#rot<-c("none", "varimax", "quartimax", "bentlerT", "geominT" , "bifactor", "promax", "oblimin", "simplimax", "bentlerQ", "geominQ" , "biquartimin" , "cluster" )
# Matrice uota che conterra le miedie degli alpha
range <- length(seq(minL,maxL,0.01))
mean.al<-matrix(0,range,length(rot))
# Sottociclo per il calcolo delle medie degli alpha (sui fattori) al variare sia della soglia sia della della rotazione
cat("Calculating the loadings thresholds \n")
for(b in 1:length(rot)){
cat("- Calculating the loadings thresholds for rotation",rot[b],"\n")
fa1<-fa(data4,fact,rotate=rot[b])
a<-fa1$loadings
class(a)<-"matrix"
colnames(a)<-paste("F",1:fact,sep="")
a<-as.data.frame(a)
a<-round(a,2)
a$D<-rownames(a)
ls1<-minL
m<-rep(0,range)
i<-1
nv<-fact
while(ls1<=maxL+0.01){
var<-lapply(1:nv,function(f)unique(a$D[abs(a[,f])>ls1]))
names(var)<-paste(colnames(a[,1:nv]))
# Do this if there are factors with length less than 2
if(any(as.numeric(summary(var)[,1])<2)){
# If a certain threshold and rotation gives only factors composed by 1 give it alpha=0
if(sum(as.numeric(summary(var)[,1])>1)==0){
m[i] <- 0
}else{
var1<-var[as.numeric(summary(var)[,1])>1]
al<-sapply(1:length(var1),function(v)alpha2(data4[,var1[[v]]])$std)
al<-data.frame(al)
#m[i]<-mean(t(al))
m[i]<-median(t(al))
}
}
# Do this if ALL the factors have length greater than 1
else{
al<-sapply(1:nv,function(v)alpha2(data4[,var[[v]]])$std)
al<-data.frame(al)
#m[i]<-mean(t(al))
m[i]<-median(t(al))
}
i<-i+1
ls1<-ls1+0.01
#cat(ls1)
}
mean.al[,b]<-m
#cat("\n")
}
# Creazione e stampa degli andamenti delle medie degli alpha
cat("Producing the threshold plot \n")
mean.al<-as.data.frame(mean.al)
colnames(mean.al)<-rot
mean.al$sl<-seq(minL,maxL,0.01)
mean.al1<-melt(mean.al,id.vars="sl")
zp<-ggplot(mean.al1,aes(x=sl,y=value,colour=variable))+geom_line()+labs(x="Soglia Loading",y="Alpha Medio",colour="Rotazione")
# Display the plot
print(zp)
max(mean.al)
#print(mean.al)
# Selezione della rotazione e della soglia che massimizzano le medie degli alpha
cat("Choosing the best rotation and threshold \n")
ind<-which(mean.al==max(mean.al),arr.ind=T)
if(class(ind)=="matrix"){
ind<-ind[1,]
}
rota<-names(mean.al)[ind[2]]
sogl<-mean.al$sl[ind[1]]
# Keep the same rotation that was selected in the first run
rot <- rota
# Calcolo fattoriale
fa1<-fa(data4,fact,rotate=rota)
a<-fa1$loadings
class(a)<-"matrix"
colnames(a)<-paste("F",1:fact,sep="")
a<-as.data.frame(a)
a<-round(a,2)
a$D<-rownames(a)
# Creazione dei fattori
var<-lapply(1:fact,function(f)unique(a$D[abs(a[,f])>sogl]))
names(var)<-paste(colnames(a[,1:fact]))
# Display the factors
cat("Displaying the factors \n")
print(var)
# togliamo le variabili che non entrano nei fattori al secondo ciclo
nc<- ncol(data4)
par1_names <- names(data4)[!(names(data4) %in% unlist(var))]
data4<-data4[,names(data4) %in% unlist(var)]
# Aggiorniamo il parametro di ciclo
par1<-nc-ncol(data4)
# togliamo le variabili che entrano in un fattore da sole (solo se non entrano in un altro fattore)
par4 <- 0
par4_names <- character()
len_fac <- cbind(1:fact,sapply(1:fact,function(v)length(var[[v]])))
if(any(len_fac[,2]==1)){
par4_nam<- data.frame(variable=as.character(unlist(var[ c(len_fac[len_fac[,2]==1,1]) ])))
par4_nam$variable <- as.character(par4_nam$variable)
par4_nam$ntimes= sapply(1:nrow(par4_nam), function(v)sum(unlist(var)%in%par4_nam[v,"variable"] ) )
# Do this only if the single variable enetrs in a variable alone
if(any(par4_nam$ntimes>1) & rot%in%obl ){
cat("- Will NOT remove variable(s)", par4_nam$variable[par4_nam$ntimes>1],"since they contribute to multiple factors","\n")
}
par4_names <- par4_nam$variable[par4_nam$ntimes==1]
par4 <- length(par4_names)
data4<-data4[,!names(data4) %in% par4_names]
}
# Togliamo le variabili che compaiono in piu fattori (se la rotazione e obliqua non effetuiamo tale operazione)
if(rota%in%obl){
par2<-0
s <- character()
}else{
s<-c(as.vector(unlist(var)))
s<-unique(s[duplicated(s)])
par2<-length(s)
data4<-data4[,!names(data4) %in% s]
}
cicl<-cicl+1
# Aggiorniamo il parametro di ciclo
par3<-par1+par2+par4
# Stampa diagnosi ciclo
cat(paste("Unused Variable:",par1),"\n")
cat("-",paste(par1_names),"\n")
cat(paste("Repeated variables:",par2),"\n")
cat("-",paste(s),"\n")
cat(paste("Single variables:",par4),"\n")
cat("-",paste(par4_names),"\n")
cat(paste("Rotation used:",rota),"\n")
cat(paste("Threshold chosen:",sogl),"\n")
cat(paste("End interation",cicl),"\n","\n")
}
cat(paste("Variables excluded in the process:"),names(data_orig)[!names(data_orig)%in%names(data4)],"\n")
return(data4)
}
#
likert_variables2 <- names(dat)
data1 <- dat[,likert_variables1[!(likert_variables1 %in% c("necessity1","educated1","reconnect.comm1", "speakersmelb.comm1", "comecloser.comm1"))]]
# Plot the correlations
corrplot(cor(data1,use = "pair"))
# check which variable does not correlated with any other vaiable
r1 <- cor(data1,use = "pair")
diag(r1) <- 0
r1 <- data.frame(r1)
temp <- data.frame(name=names(r1),cor=sapply(1:ncol(r1),function(v)any(r1[,v]>=0.3)) )
as.character(temp$name[temp$cor==F])
[1] "knowledge.instru1"
# Keep just the itemes with a r.cor greater or equal to 0.3
as <- psych::alpha(data1,check.keys=F)$item.stats
as$n1<-1:nrow(as)
summary(as$r.cor)
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.1567 0.3605 0.4448 0.4220 0.4966 0.5912
no_corr_macu <- rownames(as[abs(as$r.cor)<0.3,])
no_corr_macu
[1] "consider.ought1" "people.ought1" "expect.ought1" "fail.ought1"
data1<-data1[,!names(data1)%in%no_corr_macu]
# check which items will decrease the alpha
al<- psych::alpha(data1)
drop<-al$alpha.drop
tot<-as.numeric(al$total$std.alpha)
drop <- drop[drop$std.alpha>tot,]
drop
# Check how much
drop$std.alpha-tot
numeric(0)
# They don;t drop enough so leave it
#drop_alpha_macu <- rownames(drop)
#data1<-data1[,!names(data1)%in%drop_alpha_macu]
# check how many factors should be used
fap <- fa.parallel(data1)
Parallel analysis suggests that the number of factors = 6 and the number of components = 4
fap
Call: fa.parallel(x = data1)
Parallel analysis suggests that the number of factors = 6 and the number of components = 4
Eigen Values of
Original factors Simulated data Original components simulated data
1 5.46 0.59 6.22 1.53
2 2.26 0.46 3.08 1.44
3 0.99 0.41 1.78 1.39
4 0.54 0.36 1.36 1.34
5 0.48 0.31 1.27 1.29
6 0.28 0.26 1.02 1.24
data_macu <- data1
## Perform the anlaysis for macular thickness
#Check again the out_maculiers
out_macu <- outlier(data_macu)
#abline(h=800)
#dat_imp_pheno[out_macu>800,1:20]
#out_maculiers_macu <- dat_imp_pheno$id1[out_macu>800]
#data_macu <- data_macu[out_macu<800,]
# Run the first set of analysisi and check what is cleaned out_macu!
rot=c("oblimin","promax")
# Take off the variables that give problem
#problem_var_macu <- c( "v07_spectralis" ,"v01_cyrrus" )
#data_macu <- data_macu[,!names(data_macu)%in%problem_var_macu]
library(ggplot2)
data_macu_facleaned <- fa_all(data_macu,rot,0.2,0.5)
Calculating the number of factors needed
Parallel analysis suggests that the number of factors = 6 and the number of components = 4
Calculating the loadings thresholds
- Calculating the loadings thresholds for rotation oblimin
- Calculating the loadings thresholds for rotation promax
Producing the threshold plot
Choosing the best rotation and threshold
Displaying the factors
$F1
[1] "exciting.intr1" "improve.prof1" "speaking.prof1" "reading.prof1" "written.prof1" "listening.prof1" "overseas.post1"
$F2
[1] "dream.id1" "usewell.id1" "whenever.id1" "job.instru1" "career.instru1" "money.instru1"
$F3
[1] "converse.id1" "dream.id1" "whenever.id1" "enjoy.intr1" "life.intr1" "exciting.intr1" "challenge.intr1"
$F4
[1] "converse.id1" "time.integr1" "becomelike.integr1" "meeting.integr1" "affinity.integr1"
$F5
[1] "knowledge.instru1" "time.integr1" "meeting.integr1" "citizen.post1" "interact.post1" "overseas.post1"
[7] "globalaccess.post1"
$F6
[1] "dream.id1" "usewell.id1" "knowledge.instru1" "becomelike.integr1" "meeting.integr1" "citizen.post1"
Unused Variable: 0
-
Repeated variables: 0
-
Single variables: 0
-
Rotation used: oblimin
Threshold chosen: 0.2
End interation 1
Variables excluded in the process:
# 0 Variable do not enter the factors
not_used_fact_macu <- names(data_macu)[!names(data_macu)%in%names(data_macu_facleaned)]
not_used_fact_macu
character(0)
# Check again how many factors you need
#fa.parallel(data_macu_facleaned)
nfact_macu <- 6
# Run the actual factorial analysis on the final dataset
fa_macu<-fa(data_macu_facleaned,nfact_macu,rot="promax")
# Check whther any variable do not enter in any factor
lod <- fa_macu$loadings
class(lod) <- "matrix"
lod <- data.frame(lod)
lod$any <- apply(lod,1,function(v)any(abs(v)>=0.2) )
apply(lod[,1:nfact_macu],1,max )
converse.id1 dream.id1 usewell.id1 whenever.id1 enjoy.intr1 life.intr1 exciting.intr1
0.3826382 0.2590156 0.2313494 0.3977323 0.8472356 0.7488965 0.3882375
challenge.intr1 job.instru1 knowledge.instru1 career.instru1 money.instru1 time.integr1 becomelike.integr1
0.5021346 0.8414105 0.3784907 0.7416772 0.5841567 0.6249178 0.5377667
meeting.integr1 affinity.integr1 improve.prof1 speaking.prof1 reading.prof1 written.prof1 listening.prof1
0.4884306 0.8359326 0.7215791 0.8518862 0.6982499 0.7986566 0.8615300
citizen.post1 interact.post1 overseas.post1 globalaccess.post1
0.5709503 0.3964621 0.4730101 0.8400994
lod[lod$any==F,]
# NONE, good!
# Plot the results
a<-fa_macu$loadings
class(a)<-"matrix"
colnames(a)<-paste("F",1:nfact_macu,sep="")
a<-as.data.frame(a)
a<-round(a,2)
a$D<-rownames(a)
a1 <- a
a1$D
[1] "converse.id1" "dream.id1" "usewell.id1" "whenever.id1" "enjoy.intr1" "life.intr1"
[7] "exciting.intr1" "challenge.intr1" "job.instru1" "knowledge.instru1" "career.instru1" "money.instru1"
[13] "time.integr1" "becomelike.integr1" "meeting.integr1" "affinity.integr1" "improve.prof1" "speaking.prof1"
[19] "reading.prof1" "written.prof1" "listening.prof1" "citizen.post1" "interact.post1" "overseas.post1"
[25] "globalaccess.post1"
a1 <- melt(a1,id.vars=c("D"))
a1$x <- runif(nrow(a1))
a1$inv <- ifelse(a1$value<0,"neg","pos")
a1$value[abs(a1$value)<0.2] <- 0
a1 <- a1[a1$value!=0,]
ggplot(a1)+geom_bar(aes(x=reorder(D, value) ,y=value),stat="identity")+facet_wrap(~variable,ncol = 2,scales = "free_y")+coord_flip()
#detach("package:ggplot2", unload=TRUE)
var<-lapply(1:nfact_macu,function(f)unique(a$D[abs(a[,f])>0.2]))
names(var)<-paste(colnames(a[,1:nfact_macu]))
al <- sapply(1:length(var),function(v) psych::alpha(data_macu_facleaned[,var[[v]]])$total$std.alpha)
al
[1] 0.8740745 0.7554425 0.7210978 0.7259133 0.7286186 0.6431506
# Alpha total
psych::alpha(data_macu_facleaned)$total$std.alpha
[1] 0.8698921
# they are ok...
psych::alpha(data_macu)$total$std.alpha
[1] 0.8698921
# Table of the factors
a$D <- NULL
a[abs(a)<0.2] <- 0
for(i in 1:ncol(a)){a[,i] <- as.character(a[,i])}
a[a=="0"] <- ""
loading_fact_macu <- a
loading_fact_macu
# Discriminant analysis: In this section i will test if the values of the variables kept in the dataframe by the factorial analysis are able to discriminate between subjects for which their total score lie in the 1st and 3rd quartile.
discr<-unique(data_macu_facleaned)
# Detrmine the total score
discr$punteggio<-rowSums(discr)
# Dividce the groups of people who lie in the 4rth and 1st quarile
hist(discr$punteggio)
quantile(discr$punteggio,na.rm = T)
0% 25% 50% 75% 100%
71 99 105 112 125
discr1<-unique(discr[discr[,ncol(discr)]<=quantile(discr[,ncol(discr)],na.rm = T)[2],])
discr2<-unique(discr[discr[,ncol(discr)]>=quantile(discr[,ncol(discr)],na.rm = T)[4],])
# Wilcox Test the values of each single variable comparing the group of pople lien in the 1st and 3rd quartile
test<-data.frame(Item=colnames(discr[,1:(ncol(discr)-1)]),p.value=rep(0,(ncol(discr)-1)))
for(i in 1:(ncol(discr)-1)){
test[i,2]<-wilcox.test(discr1[,i],discr2[,i],alternative="two.sided")$p.value
}
test <- test[order(test$p.value),]
test
# they all discriminate!
# Calculate factors on the discarded variables
dat_disc <- dat[,no_corr_macu]
# check how many factors should be used
fap <- fa.parallel(dat_disc)
Parallel analysis suggests that the number of factors = 3 and the number of components = 1
fap
Call: fa.parallel(x = dat_disc)
Parallel analysis suggests that the number of factors = 3 and the number of components = 1
Eigen Values of
Original factors Simulated data Original components simulated data
1 1.72 0.64 2.21 1.11
2 0.04 0.04 0.75 1.03
3 0.01 0.00 0.67 0.97
library(ggplot2)
fa_disc <- fa(dat_disc,nfactors = 1,rotate = "oblimin")
# Plot the results
a<-fa_disc$loadings
class(a)<-"matrix"
colnames(a)<-paste("F",1,sep="")
a<-as.data.frame(a)
a<-round(a,2)
a$D<-rownames(a)
a1 <- a
a1$D
[1] "consider.ought1" "people.ought1" "expect.ought1" "fail.ought1"
a1 <- melt(a1,id.vars=c("D"))
a1$x <- runif(nrow(a1))
a1$inv <- ifelse(a1$value<0,"neg","pos")
a1$value[abs(a1$value)<0.2] <- 0
a1 <- a1[a1$value!=0,]
library(ggplot2)
ggplot(a1)+geom_bar(aes(x=reorder(D, value) ,y=value),stat="identity")+facet_wrap(~variable,ncol = 2,scales = "free_y")+coord_flip()
#detach("package:ggplot2", unload=TRUE)
# Predict the factors
pred <- as.data.frame(predict(fa_macu,dat[,names(data_macu_facleaned)]))
names(pred) <- paste("Factor",1:nfact_macu,sep = "")
# Predict the factor from the discarded variables
pred_disc <- as.data.frame(predict(fa_disc,dat[,names(dat_disc)]))
names(pred_disc) <- paste("Factor",7,sep = "")
factors <- c(names(pred),names(pred_disc))
dat_complete <- cbind(dat,scale(pred),scale(pred_disc))
corrplot(cor(dat_complete[,likert_variables2],dat_complete[,factors],use = "pair"))
all_complete <- cbind(all,pred,pred_disc)
dat_plot <- melt(all_complete,id.vars = "Context",measure.vars = factors)
library(ggplot2)
ggplot(dat_plot)+geom_boxplot(aes(x=Context,y=value,color=Context))+facet_wrap(~variable)+coord_flip()+guides(color=F)
mod <- lm(Factor1~Context,data=all_complete)
summary(mod)
Call:
lm(formula = Factor1 ~ Context, data = all_complete)
Residuals:
Min 1Q Median 3Q Max
-4.9578 -0.5538 0.2735 0.6166 1.6099
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.6961 0.1056 -6.589 1.92e-10 ***
ContextEnglish in Italy 0.8829 0.1427 6.188 1.94e-09 ***
ContextGerman in Australia 0.8869 0.1416 6.265 1.25e-09 ***
ContextItalian in Australia 0.9217 0.1499 6.147 2.45e-09 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.8839 on 308 degrees of freedom
(11 observations deleted due to missingness)
Multiple R-squared: 0.1534, Adjusted R-squared: 0.1451
F-statistic: 18.6 on 3 and 308 DF, p-value: 4.09e-11
mod <- lm(Factor2~Context,data=all_complete)
summary(mod)
Call:
lm(formula = Factor2 ~ Context, data = all_complete)
Residuals:
Min 1Q Median 3Q Max
-2.6404 -0.5853 0.0880 0.7025 1.7380
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.03317 0.10675 0.311 0.7563
ContextEnglish in Italy 0.32307 0.14416 2.241 0.0257 *
ContextGerman in Australia -0.30422 0.14304 -2.127 0.0342 *
ContextItalian in Australia -0.21141 0.15152 -1.395 0.1639
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.8932 on 308 degrees of freedom
(11 observations deleted due to missingness)
Multiple R-squared: 0.07346, Adjusted R-squared: 0.06444
F-statistic: 8.14 on 3 and 308 DF, p-value: 3.117e-05
summary(lm(Factor4~Context,data=all_complete))
Call:
lm(formula = Factor4 ~ Context, data = all_complete)
Residuals:
Min 1Q Median 3Q Max
-2.80064 -0.59875 -0.02605 0.61727 2.21437
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.2285 0.1003 2.279 0.02336 *
ContextEnglish in Italy 0.2167 0.1354 1.601 0.11050
ContextGerman in Australia -0.4162 0.1343 -3.098 0.00213 **
ContextItalian in Australia -0.7433 0.1423 -5.224 3.24e-07 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.8389 on 308 degrees of freedom
(11 observations deleted due to missingness)
Multiple R-squared: 0.1619, Adjusted R-squared: 0.1538
F-statistic: 19.84 on 3 and 308 DF, p-value: 8.779e-12
summary(lm(Factor6~Context,data=all_complete))
Call:
lm(formula = Factor6 ~ Context, data = all_complete)
Residuals:
Min 1Q Median 3Q Max
-2.26895 -0.46599 0.03875 0.47116 2.18726
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.40389 0.08773 -4.604 6.07e-06 ***
ContextEnglish in Italy 0.60408 0.11846 5.099 5.97e-07 ***
ContextGerman in Australia 0.41089 0.11755 3.496 0.000543 ***
ContextItalian in Australia 0.53121 0.12451 4.266 2.65e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.734 on 308 degrees of freedom
(11 observations deleted due to missingness)
Multiple R-squared: 0.08763, Adjusted R-squared: 0.07875
F-statistic: 9.861 on 3 and 308 DF, p-value: 3.152e-06
summary(lm(Factor7~Context,data=all_complete))
Call:
lm(formula = Factor7 ~ Context, data = all_complete)
Residuals:
Min 1Q Median 3Q Max
-1.48337 -0.66683 -0.07418 0.40868 3.15422
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.3771 0.1071 -3.521 0.000493 ***
ContextEnglish in Italy 0.4020 0.1425 2.822 0.005080 **
ContextGerman in Australia 0.4207 0.1439 2.924 0.003708 **
ContextItalian in Australia 0.6509 0.1494 4.356 1.79e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 0.8962 on 318 degrees of freedom
(1 observation deleted due to missingness)
Multiple R-squared: 0.05799, Adjusted R-squared: 0.0491
F-statistic: 6.525 on 3 and 318 DF, p-value: 0.0002699
Seven, is the number of factors that would be present according to the study design. Using very relaxed cutoff of 0.2 to get rid of not important variables in each factor.
Using very relaxed cutoff of 0.2 to get rid of not important variables in each factor.
a1 <- a1 %>% separate(D,into = c("Variable","Item"),remove=FALSE,sep=".")
Too many values at 44 locations: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, ...